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SH3-II of Drosophila Rim-binding protein with Aplip1 peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CSQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 9 291 100 mM Bicine, 2.2-2.6 M Ammoniumsulfate
Crystal Properties Matthews coefficient Solvent content 2.25 45.39
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.28 α = 90 b = 62.42 β = 90.27 c = 163.64 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX-225 2013-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.2 0.91841 BESSY 14.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.09 50 98.9 0.1 7.7 3.7 64269
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.09 2.19 92.4 0.4 2.6 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2CSQ 2.09 45.25 61256 3011 98.55 0.21005 0.20881 0.2201 0.23642 0.2455 Rfree reflections was generated in P622 and then expanded to C2 to insure equal distribution of the Rfree reflections in all six twin domains 40.754
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -2.96 1.93 12.1 -9.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.386 r_dihedral_angle_3_deg 19.63 r_dihedral_angle_4_deg 17.149 r_dihedral_angle_1_deg 5.711 r_long_range_B_refined 2.587 r_long_range_B_other 2.579 r_mcangle_it 1.359 r_mcangle_other 1.359 r_angle_other_deg 1.345 r_angle_refined_deg 1.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.386 r_dihedral_angle_3_deg 19.63 r_dihedral_angle_4_deg 17.149 r_dihedral_angle_1_deg 5.711 r_long_range_B_refined 2.587 r_long_range_B_other 2.579 r_mcangle_it 1.359 r_mcangle_other 1.359 r_angle_other_deg 1.345 r_angle_refined_deg 1.224 r_scangle_other 1.044 r_mcbond_it 0.791 r_mcbond_other 0.791 r_scbond_it 0.661 r_scbond_other 0.64 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_bond_other_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7447 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 55
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing